This old discussion again? Anyhow, I'll split the difference a bit. Of the two generations, Roger's (b. 1979-83) and Nadal's/Djokovic's (1984-88), the four overall greatest players are Roger, Novak, Rafa, and Andy - so clearly the top tier talent is better in the younger generation. But after that I think you have a group of Roddick, Safin, and Hewitt who were all lesser players than Murray* but better than anyone else in the recent generation, with a third group that includes a mixture of both (Ferrer, Ferrero, Davydenko, Nalbandian, Wawrinka, del Potro, Berdych, Tsonga).
(*Actually, Safin at his best was better than Murray I think, but less consistent)
As for the two Andys, one thing that they have in common is that their Slam records were most severely impacted by Roger Federer: Roddick was 0-4 against Roger in finals, Murray 0-3. Both are more similar to Vilas or Courier in terms of how many Slams they "should" have had, yet on the other hand it wasn't like Vilas and Courier played against weak competition to get their Slams. Connors and Borg were at their peak when Vilas won his, and you still have a strong Edberg, Becker, and Lendl, plus a rising Agassi and Sampras to contend with for Courier. Neither Roddick or Murray had that extra something to push them through in some of those Slam finals, so we are left with Slam final records like so:
Roddick: 1-4
Murray: 2-6
Compared to:
Vilas: 4-4
Courier: 4-3
All that said, I do think Murray is the overall better player. Roddick might have been better on grass, but Murray was/is better on clay and probably better on hards, or at least slow hards.